SMAPHMM: Constructor for "SMAPHMM" objects
In SMAP: A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

Description Usage Arguments Details Value Author(s) References See Also

View source: R/methods-SMAPHMM.R

A constructor for SMAPHMM-class objects.

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SMAPHMM(noStates, Phi, A=NULL,
        Pi=rep(1/noStates,noStates),
        initTrans=0.2/(noStates - 1))

`noStates`	The number of hidden states in the HMM (numeric).
`Phi`	A Gaussian distribution parameter matrix (numeric).
`A`	A `noStates * noStates` matrix of transition probabilities betweeen the hidden states (numeric).
`Pi`	A vector of initial probabilities of starting in a certain state (numeric).
`initTrans`	Specifies the transition probability between non-equal states (numeric).

Phi is a noStates * 2 matrix that specifies the paramaters of Gaussian distributions associated with each hidden state. The first column specifies standard deviations, the second specifies means.

If A == NULL, initTrans specifies the transition probability between states i and j in 1:noStates, such that i != j. Only used if A == NULL. initTrans * noStates must be smaller than (or equal to) 1.

An object of class SMAPHMM-class.

Robin Andersson, robin.andersson@lcb.uu.se

Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord, H., Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J. P., Komorowski, J., A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling, submitted

smap, SMAPHMM-class, SMAPObservations-class

SMAP documentation built on Nov. 8, 2020, 8:26 p.m.